Input data and parameters
Input
| Analysis date: | Thu May 28 10:47:58 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_08.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/00_inputs/genes.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | no |
| Protocol: | non-strand-specific |
| Sorting performed: | no |
Summary
Reads alignment
| Number of mapped reads: | 481,253 |
| Total number of alignments: | 560,893 |
| Number of secondary alignments: | 79,640 |
| Number of non-unique alignments: | 140,851 |
| Aligned to genes: | 345,883 |
| Ambiguous alignments: | 68,933 |
| No feature assigned: | 5,226 |
| Not aligned: | 18,747 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 345,883 / 98.51% |
| Intronic: | 671 / 0.19% |
| Intergenic: | 4,555 / 1.3% |
| Intronic/intergenic overlapping exon: | 14,231 / 4.05% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.7 |
Junction analysis
| Reads at junctions: | 4,467 |
| TGCT | 4.9% |
| AAAT | 3.74% |
| TGGC | 2.98% |
| CTCT | 2.96% |
| ACCA | 2.93% |
| CTGC | 2.93% |
| TCAC | 2.84% |
| AGCC | 2.55% |
| AACC | 2.42% |
| ACGT | 2.35% |
| ACGA | 2.31% |
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